BMI503: Biomedical Informatics Systems, Databases and Software Methods

Course Information

Instructor

Dr. Jaroslaw Zola

Department of Computer Science and Engineering
Department of Biomedical Informatics

Email: jzola@buffalo.edu
Web: http://www.jzola.org/
Twitter: @rzolau

Course Description

This course provides Biomedical Informatics graduate students and clinical fellows with a technical overview of the current computing and information technology systems, programming languages and software development tools available to manage, access and analyze health and biomedical data. The systems are presented in the context of effective patient care as well as research settings.

Course Organization

The course consists of a series of lectures complemented by a practical demonstrations and exercises. The course outline is provided below. Note that the course content is usually adjusted to meet students' requests, and hence it may sometimes diverge from what is below.

Student Learning Outcomes

Upon completion of the course you will gain:

Course Requirements

The course has three requirements:

  1. Class attendance and participation in in-class discussions You will be expected to read assigned material, for example journal papers, and actively engage in discussion with instructor and other students.
  2. Laboratory exercises Each course section will be complemented with graded hands-on practical exercises testing practical aspects of the covered material.
  3. Final exam The course will be concluded with open books/open notes final exam testing your knowledge from all covered topics.

Grading Policy

The final grade will be weighted average: 10% class attendance and participation, 45% laboratory exercises, 45% final exam. The number-to-letter grade mapping will be done as indicated in the table below:

Score Grade Points
90-100 A 4.0
85-89 A- 3.67
80-84 B+ 3.33
75-79 B 3.0
70-74 B- 2.67
65-69 C+ 2.33
60-64 C 2.00
55-59 C- 1.67
50-54 D 1
0-49 F 0.0

In general, no incomplete grades (IU or I) will be given. However, in special circumstances that are truly beyond your control and justify incomplete grade, we will follow the university policy on incomplete grades, available here.

Course Materials

This course does not rely on one specific textbook. However, the following book is suggested (but not required) as a complement to the lectures' content:

Additionally, several research papers may be referenced during the course.

Computing Resources

For the duration of the course you will be granted access to the resources (including storage) provided by the UB Center for Computational Research (CCR). CCR is the state-of-the-art HPC and data center hosting clusters, multi-core compute nodes, and compute nodes with GPGPU accelerators. It provides programming and execution environments supporting all types of parallelism covered in this course. Additionally, a virtual environment with a Linux distribution and all required compilers and runtime systems will be available for offline use.

Academic Integrity

Academic integrity is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university and of themselves while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. For more information, please refer to the Graduate Academic Integrity policy: http://grad.buffalo.edu/succeed/current-students/policy-library.html#academic-integrity.

Accessibility Resources

If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 716-645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web at: http://www.buffalo.edu/studentlife/who-we-are/departments/accessibility.html.

Counseling Service

As a student you may experience a range of issues that can cause barriers to learning or reduce your ability to participate in daily activities. These might include strained relationships, anxiety, high levels of stress, alcohol/drug problems, feeling down, health concerns, or unwanted sexual experiences. Counseling, Health Services and Health Promotion are here to help with these or other issues you may experience. You learn can more about these programs and services by contacting:

Counseling Services
120 Richmond Quad (North Campus), 716-645-2720
202 Michael Hall (South Campus), 716-829-5800
https://www.buffalo.edu/studentlife/who-we-are/departments/counseling.html

Health Services
Michael Hall (South Campus), 716-829-3316
https://www.buffalo.edu/studentlife/who-we-are/departments/health.html

Office of Health Promotion
114 Student Union (North Campus), 716-645-2837
https://www.buffalo.edu/studentlife/who-we-are/departments/health-promotion.html.

Sexual Violence

UB is committed to providing a safe learning environment free of all forms of discrimination and sexual harassment, including sexual assault, domestic and dating violence and stalking. If you have experienced gender-based violence (intimate partner violence, attempted or completed sexual assault, harassment, coercion, stalking, etc.), UB has resources to help. This includes academic accommodations, health and counseling services, housing accommodations, helping with legal protective orders, and assistance with reporting the incident to police or other UB officials if you so choose. Please contact UB’s Title IX Coordinator at 716-645-2266 for more information. For confidential assistance, you may also contact a Crisis Services Campus Advocate at 716-796-4399.

Please be aware UB faculty are mandated to report violence or harassment on the basis of sex or gender. This means that if you tell me about a situation, I will need to report it to the Office of Equity, Diversity and Inclusion. You will still have options about how the situation will be handled, including whether or not you wish to pursue a formal complaint. Please know that if you do not wish to have UB proceed with an investigation, your request will be honored unless UB's failure to act does not adequately mitigate the risk of harm to you or other members of the university community. You also have the option of speaking with trained counselors who can maintain complete confidentiality. UB’s Options for Confidentially Disclosing Sexual Violence provides a full explanation of the resources available, as well as contact information. You may call UB’s Office of Equity, Diversity and Inclusion at 716-645-2266 for more information, and you have the option of calling that office anonymously if you would prefer not to disclose your identity.